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This page was generated on 2022-01-21 11:08:30 -0500 (Fri, 21 Jan 2022).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo1Linux (Ubuntu 20.04.4 LTS)x86_64R Under development (unstable) (2022-01-05 r81451) -- "Unsuffered Consequences" 4163
riesling1Windows Server 2019 Standardx64R Under development (unstable) (2021-11-21 r81221) -- "Unsuffered Consequences" 4058
palomino3Windows Server 2022 Datacenterx64R Under development (unstable) (2021-12-21 r81400 ucrt) -- "Unsuffered Consequences" 4000
merida1macOS 10.14.6 Mojavex86_64R Under development (unstable) (2022-01-05 r81451) -- "Unsuffered Consequences" 4117
Click on any hostname to see more info about the system (e.g. compilers)      (*) as reported by 'uname -p', except on Windows and Mac OS X

CHECK results for RTCGAToolbox on riesling1


To the developers/maintainers of the RTCGAToolbox package:
- Please allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/RTCGAToolbox.git to
reflect on this report. See How and When does the builder pull? When will my changes propagate? here for more information.
- Make sure to use the following settings in order to reproduce any error or warning you see on this page.

raw results

Package 1664/2075HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
RTCGAToolbox 2.25.1  (landing page)
Marcel Ramos
Snapshot Date: 2022-01-20 13:55:17 -0500 (Thu, 20 Jan 2022)
git_url: https://git.bioconductor.org/packages/RTCGAToolbox
git_branch: master
git_last_commit: 80c48ec
git_last_commit_date: 2021-10-27 11:01:30 -0500 (Wed, 27 Oct 2021)
nebbiolo1Linux (Ubuntu 20.04.4 LTS) / x86_64  OK    OK    OK  UNNEEDED, same version is already published
riesling1Windows Server 2019 Standard / x64  OK    OK    OK    OK  
palomino3Windows Server 2022 Datacenter / x64  OK    OK    OK    OK  NO, package depends on 'BiocGenerics' which is not available
merida1macOS 10.14.6 Mojave / x86_64  OK    OK    OK    OK  UNNEEDED, same version is already published

Summary

Package: RTCGAToolbox
Version: 2.25.1
Command: D:\biocbuild\bbs-3.15-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:RTCGAToolbox.install-out.txt --library=D:\biocbuild\bbs-3.15-bioc\R\library --no-vignettes --timings RTCGAToolbox_2.25.1.tar.gz
StartedAt: 2022-01-20 19:56:55 -0500 (Thu, 20 Jan 2022)
EndedAt: 2022-01-20 19:59:37 -0500 (Thu, 20 Jan 2022)
EllapsedTime: 161.6 seconds
RetCode: 0
Status:   OK  
CheckDir: RTCGAToolbox.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   D:\biocbuild\bbs-3.15-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:RTCGAToolbox.install-out.txt --library=D:\biocbuild\bbs-3.15-bioc\R\library --no-vignettes --timings RTCGAToolbox_2.25.1.tar.gz
###
##############################################################################
##############################################################################


* using log directory 'D:/biocbuild/bbs-3.15-bioc/meat/RTCGAToolbox.Rcheck'
* using R Under development (unstable) (2021-11-21 r81221)
* using platform: x86_64-w64-mingw32 (64-bit)
* using session charset: ISO8859-1
* using option '--no-vignettes'
* checking for file 'RTCGAToolbox/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'RTCGAToolbox' version '2.25.1'
* package encoding: UTF-8
* checking package namespace information ... OK
* checking package dependencies ... OK
* checking if this is a source package ... OK
* checking if there is a namespace ... OK
* checking for hidden files and directories ... OK
* checking for portable file names ... OK
* checking whether package 'RTCGAToolbox' can be installed ... OK
* checking installed package size ... OK
* checking package directory ... OK
* checking 'build' directory ... OK
* checking DESCRIPTION meta-information ... OK
* checking top-level files ... OK
* checking for left-over files ... OK
* checking index information ... OK
* checking package subdirectories ... OK
* checking R files for non-ASCII characters ... OK
* checking R files for syntax errors ... OK
* checking whether the package can be loaded ... OK
* checking whether the package can be loaded with stated dependencies ... OK
* checking whether the package can be unloaded cleanly ... OK
* checking whether the namespace can be loaded with stated dependencies ... OK
* checking whether the namespace can be unloaded cleanly ... OK
* checking dependencies in R code ... OK
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... OK
* checking Rd files ... OK
* checking Rd metadata ... OK
* checking Rd cross-references ... OK
* checking for missing documentation entries ... OK
* checking for code/documentation mismatches ... OK
* checking Rd \usage sections ... OK
* checking Rd contents ... OK
* checking for unstated dependencies in examples ... OK
* checking contents of 'data' directory ... OK
* checking data for non-ASCII characters ... OK
* checking LazyData ... OK
* checking data for ASCII and uncompressed saves ... OK
* checking files in 'vignettes' ... OK
* checking examples ... OK
Examples with CPU (user + system) or elapsed time > 5s
               user system elapsed
getGISTICPeaks 5.42   0.31   10.36
biocExtract    5.19   0.33    5.51
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes in 'inst/doc' ... OK
* checking running R code from vignettes ... SKIPPED
* checking re-building of vignette outputs ... SKIPPED
* checking PDF version of manual ... OK
* DONE

Status: OK


Installation output

RTCGAToolbox.Rcheck/00install.out

##############################################################################
##############################################################################
###
### Running command:
###
###   D:\biocbuild\bbs-3.15-bioc\R\bin\R.exe CMD INSTALL RTCGAToolbox
###
##############################################################################
##############################################################################


* installing to library 'D:/biocbuild/bbs-3.15-bioc/R/library'
* installing *source* package 'RTCGAToolbox' ...
** using staged installation
** R
** data
*** moving datasets to lazyload DB
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
  converting help for package 'RTCGAToolbox'
    finding HTML links ... done
    CorResult-class                         html  
    DGEResult-class                         html  
    FirehoseCGHArray-class                  html  
    FirehoseData-class                      html  
    FirehoseGISTIC-class                    html  
    FirehoseMethylationArray-class          html  
    FirehosemRNAArray-class                 html  
    RTCGAToolbox                            html  
    accmini                                 html  
    biocExtract                             html  
    finding level-2 HTML links ... done

    getBroadSubtypes                        html  
    getCNGECorrelation                      html  
    getData                                 html  
    getDiffExpressedGenes                   html  
    getFirehoseAnalyzeDates                 html  
    getFirehoseData                         html  
    getFirehoseDatasets                     html  
    getFirehoseRunningDates                 html  
    getGISTICPeaks                          html  
    getLinks                                html  
    getMutationRate                         html  
    getReport                               html  
    getSurvival                             html  
    hg19.ucsc.gene.locations                html  
    makeSummarizedExperimentFromGISTIC      html  
    selectType                              html  
    showResults-CorResult                   html  
    showResults-DGEResult                   html  
    showResults                             html  
** building package indices
** installing vignettes
** testing if installed package can be loaded from temporary location
** testing if installed package can be loaded from final location
** testing if installed package keeps a record of temporary installation path
* DONE (RTCGAToolbox)
Making 'packages.html' ...Warning in packageDescription(i, lib.loc = lib, fields = "Title", encoding = "UTF-8") :
  DESCRIPTION file of package 'MungeSumstats' is missing or broken
Warning in packageDescription(i, lib.loc = lib, fields = "Title", encoding = "UTF-8") :
  DESCRIPTION file of package 'R453Plus1Toolbox' is missing or broken
 done

Tests output


Example timings

RTCGAToolbox.Rcheck/RTCGAToolbox-Ex.timings

nameusersystemelapsed
biocExtract5.190.335.51
getBroadSubtypes0.030.000.47
getCNGECorrelation000
getData0.000.010.01
getDiffExpressedGenes0.000.020.02
getFirehoseAnalyzeDates000
getFirehoseData000
getFirehoseDatasets000
getFirehoseRunningDates000
getGISTICPeaks 5.42 0.3110.36
getMutationRate000
getReport3.060.173.25
getSurvival0.020.000.01
makeSummarizedExperimentFromGISTIC2.250.192.42
showResults-CorResult000
showResults-DGEResult0.000.010.02
showResults000